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- PDB-9pnk: Crystal structure of the GH29-like fucosidase FucWf4 in complex w... -

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Basic information

Entry
Database: PDB / ID: 9pnk
TitleCrystal structure of the GH29-like fucosidase FucWf4 in complex with fucose
ComponentsAlpha-L-fucosidase
KeywordsHYDROLASE / fucose / fucoidan / glycoside hydrolase / fucosidase / CAZyme.
Function / homologyGlycoside hydrolase, family 29 / Alpha-L-fucosidase / alpha-L-fucosidase activity / Glycoside hydrolase superfamily / carbohydrate metabolic process / beta-L-fucopyranose / Alpha-L-fucosidase
Function and homology information
Biological speciesWenyingzhuangia fucanilytica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsHiggins, M.A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2025
Title: Structural insights into a fucosidase involved in fucoidan degradation.
Authors: Bailey, B. / Winchester, A. / McClain, D. / Clingaman, M. / Higgins, M.A.
History
DepositionJul 21, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-L-fucosidase
B: Alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,64611
Polymers120,4492
Non-polymers1,1989
Water8,323462
1
A: Alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0697
Polymers60,2241
Non-polymers8456
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,5774
Polymers60,2241
Non-polymers3533
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.785, 97.475, 123.356
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Alpha-L-fucosidase


Mass: 60224.344 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Wenyingzhuangia fucanilytica (bacteria)
Gene: AXE80_07370 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold (DE3) / References: UniProt: A0A1B1Y5Q3
#2: Sugar
ChemComp-FUL / beta-L-fucopyranose / beta-L-fucose / 6-deoxy-beta-L-galactopyranose / L-fucose / fucose / 6-DEOXY-BETA-L-GALACTOSE


Type: L-saccharide, beta linking / Mass: 164.156 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C6H12O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
LFucpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-L-fucopyranoseCOMMON NAMEGMML 1.0
b-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 462 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 41.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 18% PEG 6000, 0.12 M sodium acetate, 0.1 M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97947 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 30, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 2.19→38.88 Å / Num. obs: 52606 / % possible obs: 99.1 % / Redundancy: 8.4 % / Biso Wilson estimate: 33.8 Å2 / CC1/2: 0.994 / Net I/σ(I): 7.2
Reflection shellResolution: 2.19→2.26 Å / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4280 / CC1/2: 0.591

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.19→38.88 Å / SU ML: 0.2832 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.5445
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.229 2000 3.81 %
Rwork0.1805 50534 -
obs0.1823 52534 99.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.74 Å2
Refinement stepCycle: LAST / Resolution: 2.19→38.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7679 0 79 462 8220
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00747972
X-RAY DIFFRACTIONf_angle_d0.846510849
X-RAY DIFFRACTIONf_chiral_restr0.05431190
X-RAY DIFFRACTIONf_plane_restr0.00651385
X-RAY DIFFRACTIONf_dihedral_angle_d13.42782961
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.19-2.250.32811330.2783356X-RAY DIFFRACTION93.11
2.25-2.310.30381420.24413588X-RAY DIFFRACTION99.68
2.31-2.380.31211410.23423587X-RAY DIFFRACTION99.47
2.38-2.450.28281420.2243573X-RAY DIFFRACTION99.76
2.45-2.540.27921420.22393586X-RAY DIFFRACTION99.84
2.54-2.640.28531430.21723627X-RAY DIFFRACTION99.76
2.64-2.760.26951430.21763596X-RAY DIFFRACTION99.89
2.76-2.910.28121420.20663610X-RAY DIFFRACTION99.89
2.91-3.090.26561410.20453542X-RAY DIFFRACTION97.38
3.09-3.330.22651440.17963636X-RAY DIFFRACTION99.76
3.33-3.660.22061440.16823658X-RAY DIFFRACTION100
3.66-4.190.18231450.14523661X-RAY DIFFRACTION100
4.19-5.280.16371480.13373719X-RAY DIFFRACTION99.97
5.28-38.880.20251500.16353795X-RAY DIFFRACTION97.89

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